16.
4. To take into account
Transcription Factors vs Nucleosomes / Histone modifications
Control available?
Sequencing depth bias in Control vs IP
Different alignment methods produce different peak calling results, but the difference is
not as much as the one due to different peak caller or replicate
Many differences on peak callers can be explained by the different thresholds used
Some peak callers may be specific to some data types
Consistency may be used to set threshold if replicates are available

17.
4. To take into account
There are many tools for the analysis of ChIP-
seq data, but no standards yet

22.
5. Available tools
Uses regional averaging to mitigate sample fluctuations in the control library
Uses the control to model the distribution across the genome using the Poisson
distribution (BG). After identifying candidate peaks significantly enriched over the
BG, a local labda is estimated using windows around each peak to eliminate local
biases
Open-source, open to contributions (Artistic License) and being actively
improved
Easy to use and fast-responding developers
Compares very well to other methods